There are only 2 proper and easily available ways to remove such lines:
- decrease rendering resolution to x1(as going above is direct reason of such problems) - that should always work,
- increasing texture resolution to at least match render res multiplier - note automatic upscaling isn't the only thing to do that, texture replacement will allow you to make better textures by hand and for ui elements you don't exactly need to be an artist everyone can draw lines and boxes;p.

Forcing texture filtering to "nearest" while can also hide it, is just bad, so I wouldn't really recommend messing with it;p.

Different game ID does not make the game save corrupted. It's a mistake made by fan translators who made that full translation, but it's harmless outside of requiring different game ID for things like cwcheats. That translation has much more serious problems like text not fitting the screen or bugging out some DLC missions, but it doesn't cause any savedata problem, so if it shows as corrupted, it might as well be corrupted.

i just downloaded winDS pro apps to play VC3 but all the saves the game makes are corrupted files, my brother who also plays the game (he gave me the ISO) has no issues.
sorry if this is already ansewered but i know litle to nothing about this and i'm afraid of doing something that may break the thing
i've tried the 64bits and the 32bits